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- PDB-6gat: SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF A... -

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Basic information

Entry
Database: PDB / ID: 6gat
TitleSOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13 BP DNA CONTAINING A TGATA SITE, REGULARIZED MEAN STRUCTURE
Components
  • DNA (5'-D(*CP*AP*GP*TP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3')
  • DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*AP*CP*TP*G)-3')
  • NITROGEN REGULATORY PROTEIN AREA
KeywordsTRANSCRIPTION/DNA / DNA BINDING PROTEIN / TRANSCRIPTION FACTOR / ZINC BINDING DOMAIN / COMPLEX (TRANSCRIPTION REGULATION-DNA) / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of amide catabolic process / regulation of arginine metabolic process / regulation of nitrogen utilization / nitrate assimilation / regulation of gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II ...regulation of amide catabolic process / regulation of arginine metabolic process / regulation of nitrogen utilization / nitrate assimilation / regulation of gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Nitrogen regulatory AreA, N-terminal / Nitrogen regulatory protein AreA N terminus / Nitrogen regulatory protein areA, GATA-like domain / Fungal protein of unknown function (DUF1752) / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type ...Nitrogen regulatory AreA, N-terminal / Nitrogen regulatory protein AreA N terminus / Nitrogen regulatory protein areA, GATA-like domain / Fungal protein of unknown function (DUF1752) / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Nitrogen regulatory protein areA
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodSOLUTION NMR / simulated annealing
AuthorsClore, G.M. / Starich, M. / Wikstrom, M. / Gronenborn, A.M.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: The solution structure of the Leu22-->Val mutant AREA DNA binding domain complexed with a TGATAG core element defines a role for hydrophobic packing in the determination of specificity.
Authors: Starich, M.R. / Wikstrom, M. / Schumacher, S. / Arst Jr., H.N. / Gronenborn, A.M. / Clore, G.M.
History
DepositionNov 7, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.content_type / _pdbx_database_status.process_site / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*AP*GP*TP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3')
C: DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*AP*CP*TP*G)-3')
A: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3614
Polymers15,2963
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 34REGULARIZED MEAN STRUCTURE
Representative

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Components

#1: DNA chain DNA (5'-D(*CP*AP*GP*TP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3')


Mass: 4024.649 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*AP*CP*TP*G)-3')


Mass: 3917.559 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein NITROGEN REGULATORY PROTEIN AREA


Mass: 7353.453 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN / Mutation: L22V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Gene: POTENTIAL / Production host: Escherichia coli (E. coli) / References: UniProt: P17429
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: DATA WERE RECORDED ON A 1:1 COMPLEX

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Sample preparation

Sample conditionspH: 6.1 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5003601
Bruker DMX500BrukerDMX5006002
Bruker AMX600BrukerAMX6005003
Bruker DMX600BrukerDMX6007504
Bruker DMX750BrukerDMX7507505
Bruker AM360BrukerAM3607506
Bruker 600Bruker6007507

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR MODIFIEDMODIFIEDstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 AND PROTEIN ENGINEERING 2, 27 - 38 USING THE PROGRAM X-PLOR MODIFIED ...Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 AND PROTEIN ENGINEERING 2, 27 - 38 USING THE PROGRAM X-PLOR MODIFIED TO INCORPORATE COUPLING CONSTANT RESTRAINTS (GARRETT ET AL. (1994) J. MAGN RESON. SERIES B 104, 99 - 103), CARBON CHEMICAL SHIFT RESTRAINTS (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92 - 96) RESTRAINTS, DIPOLAR COUPLING RESTRAINTS (TJANDRA ET AL. (1997) NATURE STRUCT BIOL 4, 732-738) AND A CONFORMATIONAL DATABASE POTENTIAL FOR PROTEINS AND NUCLEIC ACIDS (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, 1067 - 1080 AND (1997) J. MAGN. RESON. 125, 171-177) THE 3D STRUCTURE OF THE COMPLEX OF THE LEU22VAL AREA DBD-DNA COMPLEX WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON THE FOLLOWING 1128 EXPERIMENTAL RESTRAINTS (A) PROTEIN: 131 SEQUENTIAL (|I-J|=1), 63 SHORT RANGE (1 < |I-J| >=5), 67 LONG RANGE (|I-J|>5), AND 38 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; NULL 120 TORSION ANGLE RESTRAINTS (53 PHI, 13 PSI, 39 CHI1, 14 CHI2, AND 1 CHI3), 39 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; NULL 75 (41 CALPHA AND 34 CBETA) 13C CHEMICAL SHIFT RESTRAINTS; NULL 49 RESIDUAL N-H DIPOLAR COUPLING RESTRAINTS; 20 DISTANCE RESTRAINTS FOR 10 BACKBONE HYDROGEN BONDS. (B) DNA: 75 INTRARESIDUE, 124 SEQUENTIAL INTRASTRAND AND 22 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 63 DISTANCES FOR WATSON-CRICK BASE PAIR HYDROGEN BONDS; 170 TORSION ANGLE RESTRAINTS FOR THE DNA BACKBONE COVERING VALUES CHARACTERISTIC OF BOTH A AND B DNA. (C) 58 INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS (D) 2 INTERMOLECULAR DISTANCE RESTRAINTS TO PHOSPHATES (E) 8 'REPULSIVE' RESTRAINTS (F) 4 DISTANCE RESTRAINTS FOR 2 INTERMOLECULAR H-BONDS BETWEEN ARG 24 AND BASE OF GUA5. THE STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED MEAN STRUCTURE AND THE LAST NUMERIC COLUMN REPRESENTS THE RMS OF THE 34 INDIVIDUAL SIMULATED ANNEALING STRUCTURES FOUND IN PDB ENTRY 8GAT ABOUT THE MEAN COORDINATE POSITIONS. THE LAST NUMERIC COLUMN IN THE INDIVIDUAL SA STRUCTURES HAS NO MEANING. THE FOLLOWING TWO SETS OF COORDINATES DEFINE THE PRINCIPAL AXIS OF THE MAGNETIC SUSCEPTIBILITY TENSOR: POINT 1 84.440-108.009-106.934 POINT 2 85.210-106.770-106.473
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 34 / Conformers submitted total number: 1

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